Various updated features

New binary with various smaller feature updates from the last years:

• per-raw-frame absolute phase estimation now accessible through GUI
• OTF interpolation error fixed
• config files are saved with fixed locale (solves issues '.' vs ',' as decimal separator)
• added a converter for experimentally obtained OTFs
• feature updates to internal components (see git log)

Rudimentary simulation support

Simulation:

• Added 'bead surface' that creates open (doughnut) and closed beads, as ground truth data for SIM
• Added a small simulation tool that generates simulated 2D, 2-beam SIM images. Not very sophisticated, but should be o.k. for basic simulation

Compatibility:
Allows for reconstructing 2x and 3x phase steps

Not much testing went into this release, so marked as 'beta' for now. Please mail or tweet if anything stopped working.

Rudimentary non-linearity support

Rudimentary support for second band not overlapping with band zero. Works o.k. for testing, but for real-world non-linear SIM, a proper band n to band n-1 estimation scheme should be implemented.

Also includes a bugfix of the parameter estimator warning in the GUI.

Better scripting support

Simplified scripts and added examples, please take a look at

org/fairsim/fiji/StepByStep.java (for Java)
scripts/ImageJ-reconstruction.bsh (for Beanshell)

This release also includes focal plane 5 from the test datasets for easy testing of the scripts. Just open the TIFF in ImageJ and run the beanshell script.

The script needs at least v.1.4.0 (this release) to work, as some additions where made to simplify it.

Image correction and parameter fit warnings

Added two features to deal with less-than-ideal data:

Image correction tab: Allows for rudimentary corrections of intensity variations between angles and phases.

Parameter estimation warning: A window will open with parameter estimation results (modulation depth estimations) and some guides how to interpret these.

New JTransforms connector

fairSIM will now connect to standard JTransforms (3.1), additionally to shipping its own fork.
The maven build will only build against JTransforms, the makefile can use both.

Mavenized fairSIM build

No new features, but fairSIM can now be build with the maven build system.

RL-deconvolution support

This version adds (preliminary) support for Richardson-Lucy-based filtering.
See their publication for more detail.
To enable the feature, use the "settings" menu for the reconstruction.

Time-lapse with parameter estimation

Time-lapse mode can now be switched to rerun the parameter estimation on every time point.

Time-lapse beta version

This version supports reconstruction time-lapse (multiple time points) SIM stacks. This is a beta release from the current development branch.